PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_009104878.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C2H2
Protein Properties Length: 379aa    MW: 43143.3 Da    PI: 7.3961
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009104878.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.10.00132143123
                    EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                    y C++Cg s s k++ ++Hi +H
  XP_009104878.1 21 YLCQYCGISRSKKYLITSHIESH 43
                    56*******************96 PP
2zf-C2H220.31.4e-066889223
                    EETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2  2 kCpdCgksFsrksnLkrHirtH 23
                    +C+ Cg  F+ + +Lk+H+++H
  XP_009104878.1 68 TCNECGAEFKKPAHLKQHMQSH 89
                    7*******************99 PP
3zf-C2H216.42.6e-0595119123
                     EEET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                     + C   dC+ s++rk++L+rH+ tH
  XP_009104878.1  95 FACYvdDCSSSYRRKDHLNRHLLTH 119
                     678888*****************99 PP
4zf-C2H2201.8e-06182205223
                     EET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2   2 kCp..dCgksFsrksnLkrHirtH 23 
                     +C+   Cgk F+ +s+L++H  +H
  XP_009104878.1 182 VCKevGCGKAFKYPSQLQKHEDSH 205
                     79999***************9888 PP
5zf-C2H220.31.5e-06272297123
                     EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                     +kC+   C+ +Fs +snL++H++  H
  XP_009104878.1 272 FKCEveGCSSTFSKPSNLQKHLKAvH 297
                     89********************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355262143IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.4646794IPR007087Zinc finger, C2H2
SMARTSM003550.00256789IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.607.0E-56885IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS0002806989IPR007087Zinc finger, C2H2
SuperFamilySSF576674.18E-1176128No hitNo description
Gene3DG3DSA:3.30.160.605.6E-1386121IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.97295124IPR007087Zinc finger, C2H2
SMARTSM003550.2195119IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028097119IPR007087Zinc finger, C2H2
SuperFamilySSF576671.9E-5122150No hitNo description
Gene3DG3DSA:3.30.160.606.0E-4122152IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551.1124149IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.598124154IPR007087Zinc finger, C2H2
PROSITE patternPS000280126149IPR007087Zinc finger, C2H2
SuperFamilySSF576678.26E-5177206No hitNo description
Gene3DG3DSA:3.30.160.609.4E-6179205IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0055181205IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.471181210IPR007087Zinc finger, C2H2
PROSITE patternPS000280183205IPR007087Zinc finger, C2H2
SMARTSM003552.2213238IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280215238IPR007087Zinc finger, C2H2
SMARTSM0035525241262IPR015880Zinc finger, C2H2-like
SuperFamilySSF576671.32E-8252307No hitNo description
PROSITE profilePS5015712.84272302IPR007087Zinc finger, C2H2
SMARTSM003553.6E-4272297IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.607.9E-8272297IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280274297IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.3E-5298324IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003554.9303329IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280305329IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005730Cellular Componentnucleolus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008097Molecular Function5S rRNA binding
GO:0046872Molecular Functionmetal ion binding
GO:0080084Molecular Function5S rDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 379 aa     Download sequence    Send to blast
MSEEAANVDV NPTKTKDIRN YLCQYCGISR SKKYLITSHI ESHHQMEVEE ERNEEACEDE  60
EEISGKQTCN ECGAEFKKPA HLKQHMQSHS LERPFACYVD DCSSSYRRKD HLNRHLLTHK  120
GKLFKCPVEN CKSEFSIHGN ISKHLKKFHN NSDSNKDDTS NGDSVNGDSQ PSGCSSGQKK  180
LVCKEVGCGK AFKYPSQLQK HEDSHVKLDS VEAFCSEIGC MKYFTNEECL KAHIRSCHQH  240
VNCEICGSKH LKKNIKRHLR THDEDSSSPG EFKCEVEGCS STFSKPSNLQ KHLKAVHEDI  300
RPFVCGFPGC GMRFAYKHVR NNHENSGSHV YTCGDFVEAD EDFTSRPRGG LKRKQVTAEM  360
LVRKRVMPPQ FDSEEQETC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5wjq_D2e-17193327284Zinc finger protein 568
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.92550.0leaf
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Both isoforms 1 and 2 transcripts are expressed in seedlings and both TFIIIA and TFIIIA-C are present at similar ratios in 10-day-old seedlings (at protein level). In correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length isoform 1 protein TFIIIA with transcriptional activity accumulates and permits de novo transcription of 5S rRNA. Isoforms 1 and 2 transcripts accumulate in various tissues of the reproductive phase, including flowers and siliques, but only isoform 2 is present in mature seeds. In flowers, both TFIIIA and TFIIIA-C are present at similar ratios (at protein level). Very low amounts of TFIIIA are found in extracts from fresh siliques compared to TFIIIA-C. The amount of full-length TFIIIA protein progressively increases from fresh siliques to seeds concomitant with lower proportions of the shorter TFIIIA-C protein (at protein level) thus leading to 5S rRNA accumulation in the seed. {ECO:0000269|PubMed:22353599}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, flowers, siliques and seeds. {ECO:0000269|PubMed:22353599}.
Functional Description ? help Back to Top
Source Description
UniProtEssential protein (PubMed:22353599). Isoform 1 is a transcription activator the binds both 5S rDNA and 5S rRNA and stimulates the transcription of 5S rRNA gene (PubMed:12711688, PubMed:22353599). Isoform 1 regulates 5S rRNA levels during development (PubMed:22353599). {ECO:0000269|PubMed:12711688, ECO:0000269|PubMed:22353599}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00229DAPTransfer from AT1G72050Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009104878.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0542250.0AY054225.1 Arabidopsis thaliana At1g72050/F28P5_6 mRNA, complete cds.
GenBankAY0660420.0AY066042.1 Arabidopsis thaliana At1g72050/F28P5_6 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009104878.10.0PREDICTED: transcription factor IIIA-like
SwissprotQ84MZ40.0TF3A_ARATH; Transcription factor IIIA
TrEMBLM4CI660.0M4CI66_BRARP; Uncharacterized protein
STRINGBra003899.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM47142852
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.20.0transcription factor IIIA